[R-SIG-Mac] Yosemite and R

[David Winsemius]

On Oct 23, 2014, at 12:12 PM, John Fox wrote:

> Hi Kevin,
> 
> Thank you for this.
> 
> As I said, I hadn't gotten around to checking into the problem -- not even looking whether someone else had reported it. I expect that the RStudio folks will address the issue, and it's probably best discussed on their website. 
> 
> I don't think that the first solution on StackOverflow is appropriate for checking packages using the RStudio Build tab, since a command like system2("pdflatex", "--help", env=paste0("PATH=", Sys.getenv("PATH"))) (adapting the suggestion on StackOverflow) simply invokes pdflatex from the current session, and doesn't modify the path for the package check. The second solution, opening RStudio from a terminal, does work but is of course awkward.

Here's an alternate discussion and It left me wondering if R.App needed the same workaround that RStudio was proposing.

http://tex.stackexchange.com/questions/208181/why-did-my-tex-related-gui-program-stop-working-in-mac-os-x-yosemite

Best;
David
> 
> Best,
> John
> 
>> -----Original Message-----
>> From: Kevin Ushey [mailto:kevinushey at gmail.com]
>> Sent: Thursday, October 23, 2014 2:23 PM
>> To: Benjamin Y Clark
>> Cc: John Fox; Simon Urbanek; r-sig-mac; Spencer Mass
>> Subject: Re: [R-SIG-Mac] Yosemite and R
>> 
>> Hi John,
>> 
>> Regarding your issue in RStudio and pdflatex -- this is a general
>> problem with any applications not launched from the terminal;
>> presumedly it would be seen in R.app as well when not launched from
>> the terminal (this is related to the forward-PATH-to-subprocesses
>> problem discussed earlier)
>> 
>> There is a prescription available on StackOverflow:
>> http://stackoverflow.com/questions/26491934/running-system-command-
>> from-r-console-cannot-locate-installed-programs-since-upg
>> 
>> Cheers,
>> Kevin
>> 
>> On Thu, Oct 23, 2014 at 11:18 AM, Benjamin Y Clark
>> <b.y.clark at csuohio.edu> wrote:
>>> Update on my issue: Upon reinstalling Xquartz, as suggested, all of
>> my previous issues went away.
>>> -Ben
>>> 
>>> --
>>> Benjamin Y. Clark, PhD
>>> Assistant Professor of Public Administration (Levin College) &
>>> Assistant Professor of Public Health (CEOMPH)
>>> Cleveland State University
>>> 
>>> Executive Committee Member
>>> Association for Budgeting and Financial Management (ABFM)
>>> 
>>> b.y.clark[at]csuohio.edu
>>> bit.ly/BenClark
>>> 
>>> 
>>> ________________________________________
>>> From: John Fox <jfox at mcmaster.ca>
>>> Sent: Thursday, October 23, 2014 2:15 PM
>>> To: 'Simon Urbanek'
>>> Cc: 'Amos B. Elberg'; 'r-sig-mac'; 'Spencer Mass'; Benjamin Y Clark;
>> 'peter dalgaard'; 'Marc Schwartz'; 'David Winsemius'; 'Hadley Wickham'
>>> Subject: RE: [R-SIG-Mac] Yosemite and R
>>> 
>>> Dear Simon,
>>> 
>>> I installed Yosemite a couple of days ago and everything seems to
>> work fine so far, including the tcltk demo that caused problems for
>> Peter, and the Rcmdr package, which gives Tcl/Tk a pretty good workout.
>> I first reinstalled XQuartz, as suggested, and I also reinstalled R and
>> updated all packages, though the latter two steps probably weren't
>> necessary. I figured that it would help to hear positive experiences as
>> well as problems.
>>> 
>>> The only issue that I've encountered so far is specific to checking
>> packages under RStudio, which doesn't appear to find pdflatex; OTOH, R
>> CMD check runs fine in a terminal window. I haven't yet tried to
>> resolve this problem.
>>> 
>>> Best,
>>> John
>>> 
>>>> -----Original Message-----
>>>> From: Simon Urbanek [mailto:simon.urbanek at r-project.org]
>>>> Sent: Tuesday, October 21, 2014 4:38 PM
>>>> To: John Fox
>>>> Cc: Amos B. Elberg; r-sig-mac; Spencer Mass; Ben Clark; peter
>> dalgaard;
>>>> Marc Schwartz; David Winsemius; Hadley Wickham
>>>> Subject: Re: [R-SIG-Mac] Yosemite and R
>>>> 
>>>> I wasn't able to reproduce but I suspect those are all red herrings
>> -
>>>> there are really no subprocesses involved at all in either case.
>>>> 
>>>> On Oct 21, 2014, at 4:19 PM, John Fox <jfox at mcmaster.ca> wrote:
>>>>> 
>>>>> Dear all,
>>>>> 
>>>>> I wonder whether this issue also accounts for the tcltk problems
>> that
>>>> have been reported. (I haven't yet upgraded to Yosemite myself,
>> hoping
>>>> to wait for the wrinkles to be ironed out, though I'll likely do so
>>>> shortly if only to see what happens.)
>>>>> 
>>>>> Best,
>>>>> John
>>>>> 
>>>>>> -----Original Message-----
>>>>>> From: r-sig-mac-bounces at r-project.org [mailto:r-sig-mac-
>> bounces at r-
>>>>>> project.org] On Behalf Of Amos B. Elberg
>>>>>> Sent: Tuesday, October 21, 2014 12:40 PM
>>>>>> To: David Winsemius; Hadley Wickham
>>>>>> Cc: r-sig-mac; Spencer Mass
>>>>>> Subject: Re: [R-SIG-Mac] Yosemite and R
>>>>>> 
>>>>>> If the full environment isn’t getting passed to R-spawned sub-
>>>>>> processes, that might explain an error I’ve been having since the
>>>>>> update:  when R is launched from the command line, calls that
>> should
>>>>>> create an X11 window in the background fail unless an X11 window
>> has
>>>>>> already been created with the width and height specified:
>>>>>> 
>>>>>>> plot(rnorm(100))
>>>>>> Error in .External2(C_X11, d$display, d$width, d$height,
>>>>>> d$pointsize,  :
>>>>>> invalid 'width' or 'height'
>>>>>>> X11()
>>>>>> Error in .External2(C_X11, d$display, d$width, d$height,
>>>>>> d$pointsize,  :
>>>>>> invalid 'width' or 'height'
>>>>>>> X11(width = 5, height = 5)
>>>>>>> plot(rnorm(100))
>>>>>> [now it  works - and any number of additional windows can be
>> spawned
>>>>>> without repeating the error]
>>>>>> [quitting R and reopening, without quitting XQuartz, and I get
>> the
>>>> same
>>>>>> error calling plot() before X11(width = , height = )
>>>>>> 
>>>>>> This does not happen in RStudio.  I don’t use the R.app gui; I
>>>> opened
>>>>>> it just now to test and I got a slew of path-related errors, but
>>>>>> they’re as likely to have to do with my not-maintained R.app as
>> with
>>>>>> anything else.
>>>>>> 
>>>>>> I had not reported this already because I wasn’t confident
>> whether
>>>> its
>>>>>> a yosemite issue, an R-patched issue, or just something odd in
>> the
>>>> way
>>>>>> I built R.
>>>>>> 
>>>>>> If incomplete-environment-passing is the new normal, is this not
>>>> going
>>>>>> to be a common issue for packages that spawn sub-processes?
>>>>>> 
>>>>>> 
>>>>>> From: Hadley Wickham <h.wickham at gmail.com>
>>>>>> Reply: Hadley Wickham <h.wickham at gmail.com>>
>>>>>> Date: October 21, 2014 at 10:12:13 AM
>>>>>> To: David Winsemius <dwinsemius at comcast.net>>
>>>>>> Cc: r-sig-mac <r-sig-mac at r-project.org>>, Spencer Mass
>>>>>> <masss at newpaltz.edu>>
>>>>>> Subject:  Re: [R-SIG-Mac] Yosemite and R
>>>>>> 
>>>>>>> No, it is not. It is expected that the path in the terminal be
>>>>>>> different to the path in R, it is _not_ expected that the path
>> in R
>>>>>> be
>>>>>>> different to the path in a subprocess started by R.
>>>>>>> 
>>>>>>> (Well it is now expected, because this appears to be a new
>> security
>>>>>>> feature in Yosemite)
>>>>>> 
>>>>>> The best thread I could find on the problem is here:
>>>>>> https://code.google.com/p/mactlmgr/issues/detail?id=102
>>>>>> 
>>>>>> --
>>>>>> http://had.co.nz/
>>>>>> 
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>> 
>>>>>>   [[alternative HTML version deleted]]
>>>>>> 
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>>>>> 
>>> 
>>> 
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David Winsemius
Alameda, CA, USA